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Redefine memory T cells in a functional manner #560

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addiehl opened this issue May 17, 2019 · 1 comment · Fixed by #623
Closed

Redefine memory T cells in a functional manner #560

addiehl opened this issue May 17, 2019 · 1 comment · Fixed by #623
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@addiehl addiehl commented May 17, 2019

This is a followup to #110.
The challenge is as currently defined TEMRA cells ('effector memory CD8-positive, alpha-beta T cell, terminally differentiated' CL:0001062) are not placed by the reasoner under the memory T cell hierarchy, as they express CD45RA and not CD45RO. As CD45RO is currently used to determine whether a T cell is a memory T cell, we should move to a functional differentia instead.

The suggest fix is to redefine memory T cell (CL:0000813) with the axiom has_completed 'memory T cell differentiation' (GO:0043379) instead of the marker axioms currently used. This functional approach will support non-human species better as well. Then all subtypes of memory T cells will receive the same axiom to allow for proper reasoning.

@addiehl addiehl added the HIPC label May 28, 2019
@addiehl addiehl self-assigned this Nov 6, 2019
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@addiehl addiehl commented Feb 10, 2020

This involved a larger set of changes, including redefining 'memory T cell', 'CD4-positive memory T cell', and 'CD8-positive memory T cell' in a phenotypic and functional manner to be broadly applicable across species, and creating 'CD4-positive memory T cell, CD45RO-positive' 9CL;0001204) and 'CD8-positive memory T cell, CD45RO-positive' (CL:0001203) human specific terms with taxon restrictions. 'effector memory CD8-positive, alpha-beta T cell, terminally differentiated' was also provided a new definition as described previously with a human taxon restriction, and 'memory CCR4-positive regulatory T cell' also received a human taxon restriction based on its makers.

addiehl added a commit that referenced this issue Feb 10, 2020
@addiehl addiehl closed this in #623 Feb 10, 2020
addiehl added a commit that referenced this issue Feb 10, 2020
memory T cell fixes #560
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